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- PDB-7bqp: The structure of HpiI -

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Basic information

Entry
Database: PDB / ID: 7bqp
TitleThe structure of HpiI
ComponentsHpiI
KeywordsBIOSYNTHETIC PROTEIN / pericyclase
Function / homology
Function and homology information


O-methyltransferase activity / secondary metabolite biosynthetic process / methylation
Similarity search - Function
O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
O-methyltransferase domain-containing protein
Similarity search - Component
Biological speciesHymenoscyphus scutula (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsCai, Y.J. / Ohashi, M. / Zhou, J.H. / Tang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)91856202 China
Ministry of Science and Technology (MoST, China)2018YFA0901900 China
CitationJournal: Nature / Year: 2020
Title: An enzymatic Alder-ene reaction.
Authors: Ohashi, M. / Jamieson, C.S. / Cai, Y. / Tan, D. / Kanayama, D. / Tang, M.C. / Anthony, S.M. / Chari, J.V. / Barber, J.S. / Picazo, E. / Kakule, T.B. / Cao, S. / Garg, N.K. / Zhou, J. / Houk, K.N. / Tang, Y.
History
DepositionMar 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HpiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5957
Polymers52,1061
Non-polymers4896
Water5,206289
1
A: HpiI
hetero molecules

A: HpiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,18914
Polymers104,2122
Non-polymers97712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_857-x+3,y,-z+5/21
Buried area14250 Å2
ΔGint-71 kcal/mol
Surface area33330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.165, 146.449, 89.845
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein HpiI


Mass: 52106.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hymenoscyphus scutula (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1F8A906*PLUS
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 6000, 5% MPD, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.33→50 Å / Num. obs: 144677 / % possible obs: 97.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 14.32 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.024 / Rrim(I) all: 0.088 / Χ2: 0.88 / Net I/σ(I): 4.2 / Num. measured all: 1905010
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.33-1.3511.51.04270180.7450.3151.090.72495.9
1.35-1.3812.30.92570280.8070.2710.9650.73196.3
1.38-1.4130.82671140.8530.2340.8590.73896.5
1.4-1.4313.60.72770420.8880.2010.7550.76196.5
1.43-1.4613.50.6171020.9180.1690.6340.77896.8
1.46-1.513.40.52371200.930.1460.5430.79796.8
1.5-1.5413.10.45671070.9430.1290.4740.81997.3
1.54-1.5812.60.39471860.9490.1150.4110.88397.3
1.58-1.6212.70.34271530.9620.0990.3560.94497.5
1.62-1.6813.60.31171870.9690.0860.3221.01797.9
1.68-1.7413.70.28172160.9750.0770.2921.12497.9
1.74-1.8113.70.24672330.980.0680.2551.25898.1
1.81-1.8913.50.22172780.9810.0620.2291.39398.5
1.89-1.9912.70.16272600.9880.0480.1691.30698.5
1.99-2.1113.40.10673040.9950.030.1111.00798.9
2.11-2.2714.10.07573520.9980.0210.0780.76999.1
2.27-2.513.80.06273750.9980.0170.0650.71199.3
2.5-2.8712.70.05374380.9980.0150.0550.6599.5
2.87-3.6113.60.04174780.9990.0110.0430.62899.8
3.61-5012.80.03476860.9990.010.0360.54199.3

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIX1.12_2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BQJ

7bqj


Resolution: 1.33→21.81 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1932 6995 5.03 %
Rwork0.1771 131958 -
obs0.1779 138953 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.77 Å2 / Biso mean: 17.9536 Å2 / Biso min: 7.63 Å2
Refinement stepCycle: final / Resolution: 1.33→21.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 32 289 3879
Biso mean--32.07 22.41 -
Num. residues----449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153699
X-RAY DIFFRACTIONf_angle_d1.3935015
X-RAY DIFFRACTIONf_chiral_restr0.109551
X-RAY DIFFRACTIONf_plane_restr0.009649
X-RAY DIFFRACTIONf_dihedral_angle_d23.9251373
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.33-1.34510.25911360.2791274760
1.3451-1.36090.26851730.2468329672
1.3609-1.37750.27051990.2411367780
1.3775-1.3950.24191980.2302412489
1.395-1.41330.24172190.2215429794
1.4133-1.43270.22762540.2147440696
1.4327-1.45310.22342120.2064442496
1.4531-1.47480.23692400.2016442697
1.4748-1.49790.23212480.1844447397
1.4979-1.52240.17922340.1844445197
1.5224-1.54870.18752470.1777447497
1.5487-1.57680.20392430.1773449297
1.5768-1.60710.20722540.1721445698
1.6071-1.63990.17892520.1691447398
1.6399-1.67560.18182600.1697451998
1.6756-1.71450.17652330.1677450798
1.7145-1.75740.18522500.1703452398
1.7574-1.80490.20662290.1768452798
1.8049-1.8580.20082440.1845452898
1.858-1.91790.21382420.1885458499
1.9179-1.98640.21742310.1939455298
1.9864-2.06590.20322460.1803458499
2.0659-2.15980.20282420.1786459299
2.1598-2.27360.17762410.1706460199
2.2736-2.41590.18932270.1683464499
2.4159-2.60210.17952500.1789462199
2.6021-2.86350.20762490.1773467199
2.8635-3.27660.19412690.18454645100
3.2766-4.12360.18772380.16934742100
4.1236-21.810.15312350.15154902100

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